Visualization of RNA-Seq results with Volcano Plot (issue with pvalue=0 & NA)

[Manolis1]

Hello,

I am using as input for the Volcano plot tool a file derived from DESeq2. The whole pipeline works great and I do get the corresponding Valcano graph but I have two little issues:

1. Few genes are highly expressed and at the same time have p-value equal to 0; thus, these genes are depicted in the corresponding Volcano at the very top:
   
   

My question is: How should I treat those genes? I definitely want to have them due to are highly expressed, but at the same time, the plot doesn`t look proper in the way they are presented. I am not saying that is wrong, just saying that is odd. Should I exclude those genes? Should I do anything else with them?

2. On some occasions the DESeq2 file that I am using as an input does show for LogFC, p-value, and p-adjust of a few genes the entry NA, I guess standing for Not Applicable, instead of any real value. Should I exclude these particular genes from the input that I am going to use for the Volcano?

I will highly appreciate any help,

Greetings

[jennaj]

Cross-posted with followup Problem with visualization of RNA-Seq results with Volcano Plot (issue with pvalue=0 & NA)